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1223 days ago

Changelog History
Page 1

  • v4.3.2 Changes

    December 10, 2020

    🚀 Detailed release notes available at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-3-2-december-10th-2020

  • v4.3.1 Changes

    October 29, 2020

    EasyBuild v4.3.1 is primarily a bugfix/update release,
    but also includes some minor enhancements.

    🚀 All details are available in the release notes, with links to the respective pull requests.

    🛠 Prominent bug fixes

    (bug fixes that warrant reinstalling easyconfigs are marked with (***))

    • 🛠 fix compatibility of EasyBuild with Python 3.9;
    • 🛠 fix various issues when using "sources" to specify extension sources;
    • (***) add patches to fix miscomputation (on POWER) and performance issues for OpenBLAS 0.3.3 through 0.3.9;
    • (***) fix source for SQLite 3.31.1;
      => incorrect source URL and filename caused SQLite 3.29.0 to be installed instead;
    • (***) configure OpenMPI 4.x (foss/2020a) with --without-verbs when using UCX;
      👀 => this fixes a warning message that occurs when using OpenMPI on systems with Infiniband, see also https://www.open-mpi.org/faq/?category=all#ofa-device-error;
    • (***) add patch for OpenMPI 3.1.4 (foss/2019b) adding device parameters for ConnectX-6;
      ⚠ => fixes warning about missing device parameters on systems with recent Infiniband cards;
    • (***) enhance OpenFOAM easyblock to add symlinks for libraries to ensure MPI versions have preference over dummy versions;
      🔧 => fixes broken tools (like snappyHexMesh) in OpenFOAM installation if EasyBuild was configured to use RPATH linking (via --rpath);
    • (***) patch out bug in collective primitive in TensorFlow 2.2.0;
    • (***) remove --no-dist-info configuration option for SIP in recent PyQt5 easyconfigs (so pip can find SIP);
    • (***) remove GLog and GFlags dependencies from PyTorch easyconfigs (known to cause problems on POWER);
    • (***) fix dependency on Bowtie of v0.x in seq2HLA easyconfigs;
    • (***) add protobuf-python as a dependency for PyTorch 1.6 (required by caffe2.python module);
    • (***) add ncurses runtime dependency to Clang easyconfigs;
    • (***) fix PyVCF easyconfig, only supports Python 2;
    • (***) remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0;
    • 👉 make OpenBLAS installation procedure respect the parallelism set by EasyBuild;
    • 🛠 fix checksum in NAMD 2.12 easyconfigs + add source URL;
    • 📇 rename jupyterhub to JupyterHub;

    Highlighted enhancements

    (enhancements that (may) warrant updating existing installations are marked with (***))

    • ✅ publish test reports to easybuild-easyblocks pull request when --include-easyblocks-from-pr is used without --from-pr;
    • ➕ add support for including easyblocks from multiple PRs at once via --include-easyblocks-from-pr;
    • ⚡️ update TensorFlow easyblock to:
      • put Bazel build files in build directory;
      • avoid unnecessary runtime patching;
      • add XLA build support;
      • leverage installed OpenSSL/BoringSSL when cURL is used as a dependency;
    • 🔧 make easyblock for installing CMake aware of --sysroot EasyBuild configuration setting;
    • ⚡️ update ScaLAPACK easyblock to support installation with CMake for recent versions (>= v2.1.0);
    • (***) use more EasyBuild installed dependencies for TensorFlow 2.2.0;
    • (***) add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for foss/2020a & iomkl/2020a);
    • (***) add additional extensions to R 4.0.0 and Bioconductor 3.11 bundle;
      ✅ => use "eb --rebuild --skip" to install the missing extensions;
    • (***) make libtirpc easier to use as replacement of rpc in glibc (for RHEL8);
    • (***) build LibTIFF with -fPIC;

    👌 Supported software

    👌 Support for installing 75 new software packages has been added, including:

    • CFDEMcoupling
    • COMSOL
    • DIRAC
    • ✅ FRUIT (Fortran Unit Test Framework)
    • GDRCopy
    • mauveAligner
    • MyCC
    • Nek5000
    • 👍 NVHPC (NVIDIA HPC SDK) + support using it as a toolchain
    • OPERA-MS
    • PyOpenCL
    • QtPy
    • SeqKit

    📦 This brings the total number of supported software packages to 2,134!
    ✅ An up-to-date list of supported software is available here.

    Easyconfigs for fosscuda/2020a and intelcuda/2020a toolchains have been added.

    ⚡️ Various software updates have been added, including:

    • ABINIT 9.2.1
    • Bazel 3.6.0
    • CUDA 11.0.2
    • GROMACS 2020.3
    • GTK+ 3.24.23
    • HMMER 3.3.1
    • Horovod 0.20.3
    • IPython 7.18.1
    • LLVM 11.0.0
    • medaka 1.1.3
    • Mesa 20.2.1
    • PSI4 1.3.2
    • PyQt5 5.15.1
    • PyRETIS 2.5.0
    • Python 3.8.6
    • ReFrame 3.2
    • Spyder 4.1.5
    • Taiyaki 5.1.0
    • TINKER 8.8.1
    • TensorFlow 2.3.1 (with foss/2019b, fosscuda/2019b, foss/2020a)
    • TRIQS 3.0.0
    • UCX 1.9.0
    • X11 20201008

    These changes result from various contributions, made by 25 different contributors:

    • 🔀 21 merged pull requests for EasyBuild framework
    • 🔀 32 merged pull requests for easyblocks
    • 🔀 287 merged pull requests for easyconfigs

    🚀 Thanks to everyone who contributed to this release in one way or another!

    ⚡️ To upgrade to EasyBuild v4.3.1, there are several options.
    Two particularly easy options include:

    • 🚀 eb --install-latest-eb-release
    • eb --from-pr 11590 # use easyconfig from PR #11590

  • v4.3.0 Changes

    September 13, 2020

    🚀 Detailed release notes available at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-3-0-september-13th-2020)

  • v4.2.2 Changes

    July 08, 2020

    🚀 Detailed release notes available at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-2-2-july-8th-2020

  • v4.2.1 Changes

    May 20, 2020

    🚀 Detailed release notes available at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-2-1-may-20th-2020

  • v4.2.0 Changes

    April 14, 2020

    🚀 EasyBuild v4.2.0 is primarily a feature/update release, but also includes various bug fixes.

    🚀 Highlights of the changes in this release include:

    ⚡️ (experimental) support for --try-update-deps, to upgrade dependencies based on available easyconfigs;

    👀 a locking mechanism to prevent two simultaneous installations of the same easyconfig file to the same installation path (see https://easybuild.readthedocs.io/en/latest/Locks.html for more information);

    significant speedup for -D/--dry-run by avoiding useless 'module show' calls;

    ✅ support for creating an index & using it to speed up searching for easyconfigs (see https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html for more information);

    ➕ additional GitHub integration features:

    • support for targeting the easyblocks and framework repositories with eb --new-pr (via --pr-target-repo)
    • support for including easyblocks from an (open) pull request via --include-easyblocks-from-pr

    - for more information, https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html

    📇 probing of external modules for missing metadata that is not provided via an external module metadata file (mostly relevant for integration with the Cray Programming Environment);

    ✅ leveraging the archspec Python library (if it is installed) to show the "code name" of the processor in your system in the output of "eb --show-system-info" and in test reports uploaded to PRs via --upload-test-report;

    👌 support for using templates like %(cudaver)s for the CUDA version (if it's included as direct dependency);

    🛠 fix for UnicodeDecodeError that was raised when reading a patch file that contained non-ASCII characters (if EasyBuild was being run with Python 3);

    🛠 fixed filtering of already installed extensions under --skip (mostly relevant for Python packages installed as bundles of extensions);

    🏗 also support %(installdir)s and %(builddir)s templates for extensions;

    take into account toolchain hierarchy when dumping easyconfig files, to avoid hardcoded subtoolchains in '*dependencies' easyconfig parameters (relevant when using --try-* options);

    take into account dependencies marked as external modules when composing template values like %(pyver)s;

    🚚 deprecate rmtree2 function provided by easybuild.tools.filetools (the remove_dir function should be used instead);

    7 new software-specific easyblocks: BerkeleyGW, CMake, ELSI, LAMMPS, libdrm, Mesa, SEPP;

    ⚡️ updates, enhancements & bug fixes for the CMakeMake, PythonPackage and PythonBundle generic easyblocks;

    ⚡️ updates, enhancements & bug fixes in the software-specific easyblocks for Clang, Ferret, Hypre, impi, libxml2, MATLAB, numexpr, OpenBabel, OpenBLAS, OpenCV, OpenFOAM, ParMETIS, PETSc, Python, QuantumESPRESSO, Qt, ROOT, Siesta, tbb, TensorFlow, TensorRT, Trinity, VMD, XCrySDen;

    ➕ added support for no less than 114 (!) new software packages, incl. ADIOS, ArviZ, Bonito, ELSI, FuSeq, GraphMap2, LAMMPS, MedPy, motionSegmentation, OpenAI-Gym, PyMC3, PyRe, PyTorch-Geometric, RAxML-NG, Shapely, STEAK, UQTk, Zip, ...;

    ⚡️ updates for already supported software, incl. Arrow 0.16.0, BUSCO 4.0.5, Clang 10.0.0, ELPA 2019.11.001, Ferret 7.5.0, GCC(core) 9.3.0, GROMACS 2020, GTK+ 3.24.13, Hypre 2.18.2, IQ-TREE 1.6.12, Java 13(.0.2), LLVM 9.0.1 + 10.0.0, likwid 5.0.1, medaka 0.12.0, numba 0.47.0, Octave 5.1.0, OpenBLAS 0.3.8, OpenBabel 3.0.0, OpenCV 4.2.0, OpenFOAM-Extend 4.1-20191120, PETSc 3.12.4, PyTorch 1.4.0, Qhull 2019.1, QuantumESPRESSO 6.5, R-bundle-Bioconductor 3.10, Racon 1.4.10, ReFrame 2.21, SLEPc 3.12.2, SimpleElastix 1.1.0, SimpleITK 1.2.4, TensorFlow 1.15.2 + 2.0.1, Trinity 2.10.0, XGBoost 0.90, xarray 0.15.1, ...;

    ⚡️ update Java/1.8 wrapper to Java/1.8.0_241;

    ✨ enhanced Java/11 wrapper to support both x86_64 and POWER;

    🛠 fixed source URL for ISL component in GCCcore easyconfigs;

    🛠 checksum fixes in easyconfigs for R 3.6.0 and 3.6.2;

    ⏪ revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs;

    🛠 fixed packaging issue that resulted in CVS easyconfigs to be missing from EasyBuild releases;

    ⚡️ updated checksum/homepage in tbb easyconfigs after move to 'oneapi-src' repository;

    ⚡️ various additional updates, enhancements & bug fixes;

    📦 This brings the total number of supported software packages to 1,912!
    ✅ An up-to-date list of supported software is available at https://easybuild.readthedocs.io/en/latest/version-specific/Supported_software.html .

    🚀 A detailed overview of all changes, which links to the respective pull requests, is available in the release notes at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-2-0-april-14th-2020 .

    These changes result from various contributions, made by 26 different contributors:

    • 🔀 56 merged pull requests for EasyBuild framework
    • 🔀 63 merged pull requests for easyblocks
    • 🔀 381 merged pull requests for easyconfigs

    🚀 Thanks to everyone who contributed to this release in one way or another!

  • v4.1.2 Changes

    April 14, 2020

    🚀 This release fixes a problem where the GitHub token that EasyBuild uses for some of the GitHub integration features (like --from-pr, --new-pr, etc.) got included in plain text in the 'top-level' EasyBuild log file when the --debug configuration option is enabled, potentially leaving it exposed to be used by others.

    We strongly encourage that you revoke the GitHub tokens you are using currently, via https://github.com/settings/tokens, and to replace them using a new token (using "eb --install-github-token --force").

    🔒 More information is available in the security advisory that was published.

    🚀 Detailed release notes at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-1-2-march-16th-2020 .

  • v4.1.1 Changes

    January 16, 2020

    🚀 This release is primarily a bug fix/update release, but it also includes a couple of minor enhancements.

    Highlights of the changes in EasyBuild v4.1.1 include:

    👌 support for "eb --show-ec" to show the contents of the specified easyconfig file, and "eb --copy-ec" to copy an easyconfig file to a specified location;

    🔧 a new --cuda-compute-capabilities configuration option, which can be used to specify with which CUDA compute capabilities GPU software should be built (for now this is only relevant for TensorFlow);

    🛠 various fixes for permission issues that occurred when (re-)installing software with EasyBuild using multiple different users;

    ⚠ avoiding needless warnings that commonly arise in EasyBuild log files;

    📦 one new software-specific easyblock for the cryptography Python package;

    🛠 various fixes for installing software on POWER systems;

    making the TensorFlow easyblock print a clear warning when no custom CUDA compute capabilities are specified (either via the new --cuda-compute-capabilities configuration option, or via the TensorFlow-specific cuda_compute_capabilities easyconfig parameter);

    - by default recent TensorFlow versions only build with the 3.5 and 7.0 CUDA compute capabilities, which implies potentially significant performance loss on systems using NVIDIA Tesla GPUs like P100;

    ⚡️ updates, enhancements & bug fixes for the Bundle, CMakeMake, conda, PythonPackage and VersionIndependentPythonPackage generic easyblocks;

    ⚡️ updates, enhancements & bug fixes for the software-specific easyblocks for Bazel, CUDA, ESMF, FSL, GCC, GROMACS, HDF5, iccifort, imkl, impi, MATLAB, MRtrix, NCL, netCDF, OpenFOAM, Python, SAMtools, SWIG, tbb, TensorFlow, WPS, and WRF;

    🛠 fixed problem that occurred when installing EasyBuild with EasyBuild running on top of Python 3;

    ➕ added support for 27 new software packages, incl. breseq, CrossMap, horton, LEMON, OpenSlide, pythran, Qualimap, ...;

    ⚡️ updates for already supported software, incl. Beast 1.10.4, Clang 9.0.1, ESMF 8.0.0, FSL 6.0.3, GDAL 3.0.2, GEOS 3.8.0, GROMACS 2019.4, GSL 2.6, Julia 1.3.1, mayavi 4.7.1, molmod 1.4.5, netCDF-C++4 4.3.1, netCDF-Fortran 4.5.2, OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMPI 4.0.2, PLUMED 2.5.3, PROJ 6.2.1, pocl 1.4, QuickFF 2.2.4, R 3.6.2 w/ foss/2019b and fosscuda/2019b, ReFrame 2.20, SAMtools 1.10, SUNDIALS 5.1.0, Salmon 1.0.0, SuiteSparse 5.6.0, TensorFlow 2.1.0 w/ fosscuda/2019b, WPS 4.1, WRF 4.1.3, ...;

    ➕ added easyconfigs for intel/2020.00 toolchain;

    ➕ added missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs;

    updated Java/1.8 wrapper to Java/1.8.0_231 (for x86_64);

    🏗 enable building of CMake in parallel;

    🏗 actually use Java dependency when building/running Bazel (rather the JDK included with Bazel);

    🛠 fix source URLs in various easyconfigs, incl. ant, libsodium, libxc, Mesa, QCA, xorg-macros, ...;

    ➕ add missing extensions in easyconfigs for cyvcf2 and pyfits;

    ➕ add alternate valid SHA256 checksums for kallisto 0.43.1 + MASS 7.3-51.4 & rda 1.0.2-2.1 extensions in R 3.6.0 easyconfigs;

    🏗 make sure we use provided Clang dependency for building pocl;

    require that sanity_pip_check is enabled in easyconfigs for Python packages that are touched by pull requests;

    👉 use True (boolean value) rather than 'True' (string value) for boolean easyconfig parameters;

    ⚡️ various additional updates, enhancements & bug fixes;

    📦 This brings the total number of supported software packages to 1,798!
    ✅ An up-to-date list of supported software is available at https://easybuild.readthedocs.io/en/latest/version-specific/Supported_software.html .

    🚀 A detailed overview of all changes, which links to the respective pull requests, is available in the release notes at https://easybuild.readthedocs.io/en/latest/Release_notes.html .

    These changes result from various contributions, made by 22 different contributors:

    • 🔀 27 merged pull requests for EasyBuild framework
    • 🔀 47 merged pull requests for easyblocks
    • 🔀 197 merged pull requests for easyconfigs

    🚀 Thanks to everyone who contributed to this release in one way or another!

  • v4.1.0

    December 04, 2019

  • v4.0.1

    October 18, 2019